Not really cupping, more like scalloping caused by the tire's tread. Totally normal and there is no way to avoid that I know of other than eliminating the tread cuts (a smooth or 'slick' tire). Cupping is a random pattern, not tied into the tread pattern.
Some people take a rasp or a Surfoam to the tire to knock down those bumps; it is a little risky 'cause you have to have the bike running and in gear on the centerstand while you grind away at the rear tire.

Another way to take down those high spots is to use a tire balancer to mount the tire (and wheel), and then a hand grinder to both grind and spin the tire. Sort of like a poor man's lathe.
By the way, girlie- men use the file in first gear while <real> men try fourth or fifth.

The truly tough folks get someone else to ride the bike while they hang off the luggage rack and whittle away....
Usually the wear pattern you seem to have (tread block feathering is what it really is) does not cause any difficulty and is not even something you can feel when riding.
Brian
Can someone explain to me the rippling affect along the center line of my rear tire? I'm wearing PR3, and there appears, along the center threads (guess about 2.5" wide), a rippling of evenly spaced "bumps" all the way around. Is this what I sometimes see referred to as "cupping?"